In a statement, the State Department said Secretary of State Rex W. Tillerson had not made a final decision about the future of the office. But it noted that he has expressed skepticism about the proliferation of special envoys during the Obama administration, saying they could strip expertise from the regional bureaus. Other officials said the process of folding in the office had already begun.
The special representative played a diminishing role in recent years as the Afghan war faded from the headlines. Its staff had dwindled even before Mr. Obama left office, as his secretary of state, John Kerry, weighed folding the office back into the departments bureaucracy.
But the Trump administrations decision to do so now, at the very moment it is devising a strategy for Afghanistan, underlines the Pentagons outsize role in the process. Last week, President Trump authorized Defense Secretary Jim Mattis to send thousands of additional troops into a war that currently engages 8,800 American troops.
The awkward timing was not lost on Mr. Trumps critics.
The Pentagon is contemplating more war in Afghanistan, while the State Department is shutting down the office that could give it a voice in that important development, said Vali R. Nasr, who was a senior adviser on Pakistan in the office between 2009 and 2011.
Mr. Holbrooke, who died in December 2010, had a turbulent relationship with Mr. Obamas White House. But he assembled a team of experts from the Pentagon, the C.I.A., the Agriculture Department and other agencies to devise a civilian strategy for stabilizing Afghanistan that was designed to complement Mr. Obamas military surge of 30,000 troops in 2009.
Among those on Mr. Holbrookes staff, in addition to Mr. Nasr, were Rina Amiri, an Afghan-born woman who advocated on behalf of womens rights in her native country, and Barnett R. Rubin, a prominent scholar on Afghanistan and the Taliban at New York University.
Mr. Holbrooke also initiated contacts with the Taliban about negotiating a political settlement with the Afghan government, a process he said would have to involve neighboring Pakistan. Nine years later, many experts on Afghanistan say a settlement between Kabul and the Taliban remains one of the few options for bringing lasting peace to the country.
The special representatives office elevated the importance of the diplomatic and political equities to be on par with the military equities, said Daniel F. Feldman, who served as Mr. Holbrookes deputy and later became the special representative himself. What were still bereft of is any strategy for whats going to lead to stability in Afghanistan.
Mr. Trumps decision to authorize the Pentagon to deploy more troops was a stopgap measure, driven by worries that the Taliban were making gains on the battlefield and that the government of President Ashraf Ghani of Afghanistan was in danger of falling. On Friday, a series of deadly bombings in Pakistan added to the sense of regional instability.
The White House National Security Council has met multiple times to work on a broader strategy. It is being labeled a South Asia policy, to distinguish it from the Obama administrations so-called Af-Pak policy. Mr. Mattis has said he hopes to present the strategy by mid-July.
Mr. Tillerson and his chief of staff, Margaret Peterlin, attended at least one meeting last week, people briefed on the process said. But the State Department did not send an Afghanistan subject expert to the meeting, a practice that officials say has become commonplace under Mr. Tillerson.
Mr. Tillerson and Ms. Peterlin did not brief the special representatives office about the meetings, and even now, the departments Afghan experts are not certain what role they are supposed to play in enacting the policy.
The problems are compounded by a lack of senior people in the State Departments Bureau of South and Central Asian Affairs. It currently has no assistant secretary, even one to serve on an acting basis, and only an acting ambassador in Kabul. In effect, there is no expert at the department on Afghanistan above the level of the Afghan office director.
Some diplomats said the staffing vacuum, rather than the end of the special representatives office, is the problem.
Consolidation makes a lot of sense from a policy point of view, Mr. Carpenter said, but in the end, its all about the right personnel, and I trust they have a plan to put the right senior officials in these positions.
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A version of this article appears in print on June 24, 2017, on Page A5 of the New York edition with the headline: State Dept. Moves to Close Afghan Strategy Office.
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State Dept. Moves to Shut Office Planning Afghanistan Strategy - New York Times